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Biomedical subjects

Ping Liang

Publications and source records attributed to Ping Liang.

At least 19 recordsLinked to original sources

Interleukin-31 and oncostatin-M mediate distinct signaling reactions and response patterns in lung epithelial cells.

Lung epithelial cells are primary targets of oncostatin M (OSM) and, to a lower degree, of interleukin (IL)-6 and IL-31, all members of the IL-6 cytokine family. The OSM receptor (OSMR) signals through activation of STAT and mitogen-activated protein kinase pathways to induce genes encoding differentiated cell functions, reduce cell-cell interaction, and suppress cell proliferation. IL-31 functions through the heteromeric IL-31 receptor, which shares with OSMR the OSMRbeta subunit, but does not engage gp130, the common subunit of all other IL-6 cytokine receptors. Because the response of epithelial cells to IL-31 is unknown, the action of IL-31 was characterized in the human alveolar epithelial cell line A549 in which the expression of the ligand-binding IL-31Ralpha subunit was increased. IL-31 initiated signaling that differed from other IL-6 cytokines by the particularly strong recruitment of the STAT3, ERK, JNK, and Akt pathways. IL-31 was highly effective in suppressing proliferation by altering expression of cell cycle proteins, including up-regulation of p27(Kip1) and down-regulation of cyclin B1, CDC2, CDK6, MCM4, and retinoblastoma. A single STAT3 recruitment site (Tyr-721) in the cytoplasmic domain of IL-31Ralpha exerts a dominant function in the entire receptor complex and is critical for gene induction, morphological changes, and growth inhibition. The data suggest that inflammatory and immune reactions involving activated T-cells regulate functions of epithelial cells by IL-6 cytokines through receptor-defined signaling reactions.

Brain Neoplasms↗

Development of autoimmunity in IL-14alpha-transgenic mice.

Multiple genetic loci contribute to the development of systemic lupus erythematosus (SLE). In murine models for SLE, various genes on chromosome four have been implicated. IL-14 is a cytokine originally identified as a B cell growth factor. The il14 gene is located on chromosome 4. IL-14alpha is a cytokine encoded by the plus strand of the IL-14 gene using exons 3-10. The expression of IL-14alpha is increased in (NZB x NZW)F1 mice. In this study, we produced IL-14alpha-transgenic mice to study the role of IL-14alpha in the development of autoimmunity. At age 3-9 mo, IL-14alpha-transgenic mice demonstrate increased numbers of B1 cells in the peritoneum, increased serum IgM, IgG, and IgG 2a and show enhanced responses to T-dependent and T-independent Ags compared with littermate controls. At age 9-17 mo, IL-14alpha-transgenic mice develop autoantibodies, sialadenitis, as in Sjögren's syndrome, and immune complex-mediated nephritis, as in World Health Organization class II SLE nephritis. Between the ages 14-18 mo, 95% of IL-14alpha-transgenic mice developed CD5+ B cell lymphomas, consistent with the lymphomas seen in elderly patients with Sjögren's syndrome and SLE. These data support a role for IL-14alpha in the development of both autoimmunity and lymphomagenesis. These studies may provide a genetic link between these often related disorders.

Age Factors↗

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons.

The long interspersed element-1 (LINE-1 or L1) is a highly successful retrotransposon in mammals. L1 elements have continued to actively propagate subsequent to the human-chimpanzee divergence, approximately 6 million years ago, resulting in species-specific inserts. Here, we report a detailed characterization of chimpanzee-specific L1 subfamily diversity and a comparison with their human-specific counterparts. Our results indicate that L1 elements have experienced different evolutionary fates in humans and chimpanzees within the past approximately 6 million years. Although the species-specific L1 copy numbers are on the same order in both species (1200-2000 copies), the number of retrotransposition-competent elements appears to be much higher in the human genome than in the chimpanzee genome. Also, while human L1 subfamilies belong to the same lineage, we identified two lineages of recently integrated L1 subfamilies in the chimpanzee genome. The two lineages seem to have coexisted for several million years, but only one shows evidence of expansion within the past three million years. These differential evolutionary paths may be the result of random variation, or the product of competition between L1 subfamily lineages. Our results suggest that the coexistence of several L1 subfamily lineages within a species may be resolved in a very short evolutionary period of time, perhaps in just a few million years. Therefore, the chimpanzee genome constitutes an excellent model in which to analyze the evolutionary dynamics of L1 retrotransposons.

5' Untranslated Regions↗

Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies.

Mobile elements represent a relatively new class of markers for the study of human evolution. Long interspersed elements (LINEs) belong to a group of retrotransposons comprising approximately 21% of the human genome. Young LINE-1 (L1) elements that have integrated recently into the human genome can be polymorphic for insertion presence/absence in different human populations at particular chromosomal locations. To identify putative novel L1 insertion polymorphisms, we computationally compared two draft assemblies of the whole human genome (Public and Celera Human Genome assemblies). We identified a total of 148 potential polymorphic L1 insertion loci, among which 73 were candidates for novel polymorphic loci. Based on additional analyses we selected 34 loci for further experimental studies. PCR-based assays and DNA sequence analysis were performed for these 34 loci in 80 unrelated individuals from four diverse human populations: African-American, Asian, Caucasian, and South American. All but two of the selected loci were confirmed as polymorphic in our human population panel. Approximately 47% of the analyzed loci integrated into other repetitive elements, most commonly older L1s. One of the insertions was accompanied by a BC200 sequence. Collectively, these mobile elements represent a valuable source of genomic polymorphism for the study of human population genetics. Our results also suggest that the exhaustive identification of L1 insertion polymorphisms is far from complete, and new whole genome sequences are valuable sources for finding novel retrotransposon insertion polymorphisms.

Alleles↗

Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome.

BACKGROUND: Coordinately regulated genes often physically cluster in eukaryotic genomes, for reasons that remain unclear. RESULTS: Here we provide evidence that many S. cerevisiae genes induced by starvation and other stresses reside in non-random clusters, where transcription of these genes is repressed in the absence of stress. Most genes essential for growth or for rapid, post-transcriptional responses to stress in cycling cells map between these gene clusters. Genes that are transcriptionally induced by stresses include a large fraction of rapidly evolving paralogues of duplicated genes that arose during an ancient whole genome duplication event. Many of these rapidly evolving paralogues have acquired new or more specialized functions that are less essential for growth. The slowly evolving paralogues of these genes are less likely to be transcriptionally repressed in the absence of stress, and are frequently essential for growth or for rapid stress responses that may require constitutive expression of these genes in cycling cells. CONCLUSION: Our findings suggest that a fundamental organizing principle during evolution of the S. cerevisiae genome has been clustering of starvation and other stress-induced genes in chromosome regions that are transcriptionally repressed in the absence of stress, from which most genes essential for growth or rapid stress responses have been excluded. Chromatin-mediated repression of many stress-induced genes may have evolved since the whole genome duplication in parallel with functions for proteins encoded by these genes that are incompatible with growth. These functions likely provide fitness effects that escape detection in assays of reproductive capacity routinely employed to assess evolutionary fitness, or to identify genes that confer stress-resistance in cycling cells.

Evolution, Molecular↗

Human genomic deletions mediated by recombination between Alu elements.

Recombination between Alu elements results in genomic deletions associated with many human genetic disorders. Here, we compare the reference human and chimpanzee genomes to determine the magnitude of this recombination process in the human lineage since the human-chimpanzee divergence approximately 6 million years ago. Combining computational data mining and wet-bench experimental verification, we identified 492 human-specific deletions (for a total of approximately 400 kb) attributable to this process, a significant component of the insertion/deletion spectrum of the human genome. The majority of the deletions (295 of 492) coincide with known or predicted genes (including 3 that deleted functional exons, as compared with orthologous chimpanzee genes), which implicates this process in creating a substantial portion of the genomic differences between humans and chimpanzees. Overall, we found that Alu recombination-mediated genomic deletion has had a much higher impact than was inferred from previously identified isolated events and that it continues to contribute to the dynamic nature of the human genome.

Animals↗

Determination of desoxyepothilone B in nude mice plasma by liquid-liquid extraction and reversed-phase high-performance liquid chromatography.

A novel reversed-phase high-performance liquid chromatographic (HPLC) method has been established for the determination of a newly developed anti-cancer agent desoxyepothilone B (dEpo B) in nude mice plasma. The sample preparation involved deproteination of 200 microl of plasma sample first, followed by liquid-liquid extraction of the resultant supernatant with chloroform. The compound taxol was used as the internal standard. Chromatographic separations were carried out on a 250 mm x 4.6 mm Zorbax SB-phenyl column with acetonitrile-0.25% orthophosphoric acid (50/50, v/v) as mobile phase and UV detection at 250 nm. For dEpo B and taxol at the concentration level of 10 microg/ml in nude mice plasma, the absolute extraction recoveries were 85.3 and 87.2%, respectively. The linear quantification range of the method was 0.1-100 microg/ml in nude mice plasma with linear correlation coefficients greater than 0.999. The within-day and between-day relative standard deviations (R.S.D.s) for dEpo B at 0.5, 2.5 and 10 microg/ml levels in nude mice plasma fell in the range of 2.8-4.8 and 1.5-4.6%, and the within-day and between-day recoveries were in the range of 96.5-101.7 and 97.7-101.2%, respectively.

Animals↗

[Long-term results of percutaneous sonographically-guided microwave ablation therapy of early-stage hepatocellular carcinoma].

OBJECTIVE: To evaluate the long-term results of percutaneous microwave coagulation therapy in the treatment of early hepatocellular carcinoma. METHODS: From May 1994 to June 2004, a total of 216 patients with 275 nodules of hepatocellular carcinoma whose diameter <or= 5 cm had undergone percutaneous microwave coagulation therapy (193 men, 23 women; mean age, 54.68 years). Institute review board approval and informed consent were obtained. Complete tumor necrosis rates, long-term survival rates, recurrence rates and the complications of the patients were analyzed. RESULTS: The mean follow-up period after microwave ablation was 40 months +/- 24 (range, 6 - 127 months). One hundred fifty-nine remained alive and consulted our hospital periodically as outpatients. Fifty-seven patients died. Complete tumor necrosis was seen in 95.64% (263/275) patients. One, 2, 3, 4 and 5-year cumulative survival rates were 94.87%, 88.81%, 80.44%, 74.97% and 68.63%, respectively. One, 2, 3, 4 and 5-year cumulative recurrence rates were 20.01%, 32.04%, 39.57%, 44.97% and 52.90%, respectively. Three patients have severe complications, including needle track implantation in one patient, biliary fistula in two patients. One patient died of pulmonary infection one week after the treatment. CONCLUSION: Sonographically-guided microwave coagulation therapy could make complete tumor necrosis in most cases of early hepatocellular carcinoma with low incidence of complications and this method has satisfactory long-term curative effect.

Adult↗

[Evaluation of long-term therapeutic effects of ultrasound-guided percutaneous microwave ablation of liver metastases].

OBJECTIVE: To explore therapeutic results of local microwave ablation for hepatic metastasis and the factors influencing the survival after percutaneous microwave ablation therapy. METHODS: From July 1995 to June 2005 128 patients with 282 hepatic metastases nodules with the primary diseases of upper gastrointestinal tumor (n = 26), colorectal tumor (n = 44), breast carcinoma (n = 19), pulmonary carcinoma (n = 15), and malignant tumor in other part of the body (n = 24), underwent percutaneous microwave ablation therapy and were followed up for 29.7 +/- 19.9 months (1 - 103 months). The largest diameter of the metastatic nodules was 3.5 +/- 1.6 cm (0.7 - 8.6 cm). Sixty-four cases had 140 nodules 3.0 cm in diameter. Forty-seven patients had single nodule, 44 patients had 2 nodules, and 93 patients had 3 or more nodules. Fifty-seven patients had tumor of low differentiation, 53 had tumor of middle differentiation, and 18 had highly differentiated tumors. Kaplan-Meier method was used to calculate the cumulative survival rate. Statistical comparison of the effects of potential predictive factors on survival rate was performed using log-rank analysis. Multivariate analysis of the survival rates was performed by using Cox's proportional hazard model. RESULTS: The 1, 2, 3, 4, and 5-year cumulative survival rates of all 128 patients were 90.88%, 73.84%, 51.09%, 36.14%, and 31.89% respectively. Univariate analysis showed that tumor size (P = 0.028), tumor differentiation (P = 0.026) and local recurrence or new metastases (P < 0.001) significantly affected the survival. Multivariate analysis revealed that tumor size (P = 0.035), recurrence or new metastases (P = 0.001) and tumor differentiation (P = 0.038) each had a significant effect on survival. CONCLUSION: There is a significantly higher probability of long-term survival for patients with well-differentiated tumors 3.0 cm or less in diameter and without recurrence or new metastasis after percutaneous microwave ablation.

Adult↗

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms.

Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended "NT-AARA" motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes.

Alu Elements↗

dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans.

Retrotransposons constitute over 40% of the human genome and play important roles in the evolution of the genome. Since certain types of retrotransposons, particularly members of the Alu, L1, and SVA families, are still active, their recent and ongoing propagation generates a unique and important class of human genomic diversity/polymorphism (for the presence and absence of an insertion) with some elements known to cause genetic diseases. So far, over 2,300, 500, and 80 Alu, L1, and SVA insertions, respectively, have been reported to be polymorphic and many more are yet to be discovered. We present here the Database of Retrotransposon Insertion Polymorphisms (dbRIP; http://falcon.roswellpark.org:9090), a highly integrated and interactive database of human retrotransposon insertion polymorphisms (RIPs). dbRIP currently contains a nonredundant list of 1,625, 407, and 63 polymorphic Alu, L1, and SVA elements, respectively, or a total of 2,095 RIPs. In dbRIP, we deploy the utilities and annotated data of the genome browser developed at the University of California at Santa Cruz (UCSC) for user-friendly queries and integrative browsing of RIPs along with all other genome annotation information. Users can query the database by a variety of means and have access to the detailed information related to a RIP, including detailed insertion sequences and genotype data. dbRIP represents the first database providing comprehensive, integrative, and interactive compilation of RIP data, and it will be a useful resource for researchers working in the area of human genetics.

Databases, Genetic↗

Mutational data integration in gene-oriented files of the Hermansky-Pudlak Syndrome database.

Hermansky-Pudlak Syndrome (HPS) is a genetically heterogeneous disorder characterized by oculocutaneous albinism and prolonged bleeding due to abnormal vesicle trafficking to lysosomes and related organelles such as melanosomes and platelet dense granules. This HPS database (HPSD; http://liweilab.genetics.ac.cn/HPSD/) provides integrated, annotatory, and curative data that is distributed in a variety of public databases or predicted by bioinformatics servers for the recently cloned human and mouse HPS genes, as well as for the genes responsible for HPSrelated syndromes, such as ChediakHigashi Syndrome (CHS), Griscelli syndrome (GS), oculocutaneous albinism (OCA), Usher syndrome type 1B (USH1B), and ocular albinism (OA). The HPSD is designed by using a unique GeneOriented File (GOF) format. Seven blocks (genomic, transcript, protein, function, mutation, phenotype, and reference) are carefully annotated in each userfriendly GOF entry. The HPSD emphasizes paired human and mouse GOF entries. The genes included in this database (currently 58 in total) are arbitrarily divided into four categories: 1) Human and Mouse HPS, 2) Mouse HPS Only, 3) Putative Mouse or Human HPS, and 4) HPS Related Syndromes. All the mutations in these genes are integrated in the GOFs. We expect that these very informative and peerreviewed GOFs will be shortcuts to utilize the webbased information for the emerging interdisciplinary studies of HPS.

Animals↗

Distinct patterns of germ-line deletions in MLH1 and MSH2: the implication of Alu repetitive element in the genetic etiology of Lynch syndrome (HNPCC).

A relatively high frequency of germ-line genomic rearrangements in MLH1 and MSH2 has been reported among Lynch Syndrome (HNPCC) patients from different ethnic populations. To investigate the underlying molecular mechanisms, we characterized the DNA breakpoints of 11 germ-line deletions, six for MLH1 and five for MSH2. Distinct deletion patterns were found for the two genes. The five cases of MSH2 deletions result exclusively from intragenic unequal recombination mediated by repetitive Alu sequences. In contrast, five out of the six MLH1 deletions are due to recombinations involving sequences of no significant homology (P=0.015). A detailed analysis of the DNA breakpoints in the two genes, previously characterized by other groups, validated the observation that Alu-mediated unequal recombination is the main type of deletion in MSH2 (n=34), but not in MLH1 (n=21) (P<0.0001). Plotting the distribution of known DNA breakpoints among the introns of the two genes showed that, the highest breakpoint density is co-localized with the highest Alu density. Our study suggests that Alu is a promoting factor for the genomic recombinations in both MLH1 and MSH2, and the local Alu density may be involved in shaping the deletion pattern.

Adaptor Proteins, Signal Transducing↗

Evidence for ORC-dependent repression of budding yeast genes induced by starvation and other stresses.

The highly conserved origin recognition complex (ORC) is required for repressing genes in the silent mating type loci of budding yeast. Here we report that at a non-permissive temperature, the temperature-sensitive orc2-1 mutation induces the expression of more than 500 genes, the majority of which are also induced during starvation of wild-type cells. Many genes induced by starvation or by the orc2-1 mutation are also induced by inactivation of proteins required for chromatin-mediated repression of transcription. Genes induced by the orc2-1 mutation, starvation, or inactivation of repressor proteins, map near ORC-binding loci significantly more frequently compared to all genes. Genes repressed by starvation map near ORC-binding sites less frequently compared to all genes, which suggests they have been evolutionarily excluded from regions of repressive chromatin near ORC-binding sites. Deletion of sequences containing ORC-binding sites near the DAL2 and DAL4 genes in the DAL gene cluster, which are induced by either the orc2-1 mutation or by starvation, constitutively activates these genes and abolishes their activation by the orc2-1 mutation. Our findings suggest a role for ORC in the repression of a large number of budding yeast genes induced by starvation or other aspects of a deleterious environment.

Apoptosis↗

[Influence of microwave ablation and surgical resection of small primary hepatocellular carcinoma on hematogenous dissemination of tumor cells].

OBJECTIVE: To study the influence of percutaneous microwave ablation (PMA) and surgical resection for patients with small primary hepatocellular carcinoma (PHC) on dissemination of tumor cells in peripheral blood determined by AFP mRNA. METHODS: Forty patients with small PHC (The maximal diameter < or = 5 cm) confirmed histologically were included in this study. All the patients had single tumor nodule only without metastasis. Of the 40 patients, 19 were treated by PMA and 21 by surgical resection. Blood samples were collected and tested immediately before treatment, 30 min after the mass ablated/resected, 1 d and 7 d later by RTD-Nested-RT-PCR for AFP mRNA. The CD3, CD4, CD8 and CD4/CD8 in blood, and hepatic function were tested at the same time points as well. RESULTS: After treatment, ALT and AST in peripheral blood increased in both groups, but more intensely in the surgical group. The CD3, CD4 and CD4/CD8 in peripheral blood decreased at 30 min, 1 day and 7 days after surgical resection, and the lowest value was at 30 min after surgery. The immune function was kept at the same level as pre-treatment in the PMA group. AFP mRNA copies in blood could be detected in 27 of 40 patients (67.5%) in two groups before treatment, and the copy number was increased after treatment. There was no significant difference between the two groups. The patients were followed up for 1 - 16 months. AFP mRNA copies in blood could be detected persistently in the 4 patients with extrahepatic metastasis or liver recurrence. CONCLUSION: Surgical resection and microwave ablation may cause PHC cells dissemination into the blood circulation in patients with small PHC, and there was no difference between the two treatment groups. The cellular immune function in peripheral blood is decreased after surgical resection, but is maintained at the same level as pre-treatment in the PMA group. The impairment of liver function is less severe after PMA treatment than surgical resection. PMA may provide certain value for clinical management of small hepatocellular carcinoma.

Adult↗

Mechanism of neurophysiological treatment of amblyopia using functional magnetic resonance imaging.

PURPOSE: To research the mechanism of neurophysiological treatment of amblyopia by observing the visual cortex activation under rotating grating stimulus with functional magnetic resonance imaging (MRI), and identify the components of the activation. METHODS: Nine healthy volunteers were examined using gradient-recalled echo and echo-planar imaging (GRE-EPI) pulse sequence performed at the 1.5 Tesla MRI scanner. In the block designing, rotating grating, stationary grating and luminance were plotted as task states, stationary grating, luminance and darkness as control states, respectively. The tasks of stimuli included 6 steps. Imaging processing and statistical analysis were carried out off-line using statistical parametric mapping (SPM99) software in single-subject. RESULTS: Some individual areas of visual cortex were activated by various stimuli information supplied by rotating grating. The strong activation in the middle of occipital lobe related to the stimuli of luminance, bilateral activation of Brodmann's 19th area related to visual motion perception, and the mild activation in the middle of occipital lobe related to form perception. CONCLUSION: The plotting of control state is important in bock design. The effective visual information of rotating grating includes components of luminance, visual motion perception and form perception. Functional MRI has potential as a tool for studying the physiological mechanism of visual cortex.

Adult↗

Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

BACKGROUND: The rTS gene (ENOSF1), first identified in Homo sapiens as a gene complementary to the thymidylate synthase (TYMS) mRNA, is known to encode two protein isoforms, rTSalpha and rTSbeta. The rTSbeta isoform appears to be an enzyme responsible for the synthesis of signaling molecules involved in the down-regulation of thymidylate synthase, but the exact cellular functions of rTS genes are largely unknown. RESULTS: Through comparative genomic sequence analysis, we predicted the existence of a novel protein isoform, rTS, which has a 27 residue longer N-terminus by virtue of utilizing an alternative start codon located upstream of the start codon in rTSbeta. We observed that a similar extended N-terminus could be predicted in all rTS genes for which genomic sequences are available and the extended regions are conserved from bacteria to human. Therefore, we reasoned that the protein with the extended N-terminus might represent an ancestral form of the rTS protein. Sequence analysis strongly predicts a mitochondrial signal sequence in the extended N-terminal of human rTSgamma, which is absent in rTSbeta. We confirmed the existence of rTS in human mitochondria experimentally by demonstrating the presence of both rTSgamma and rTSbeta proteins in mitochondria isolated by subcellular fractionation. In addition, our comprehensive analysis of rTS orthologous sequences reveals an unusual phylogenetic distribution of this gene, which suggests the occurrence of one or more horizontal gene transfer events. CONCLUSION: The presence of two rTS isoforms in mitochondria suggests that the rTS signaling pathway may be active within mitochondria. Our report also presents an example of identifying novel protein isoforms and for improving gene annotation through comparative genomic analysis.

Amino Acid Sequence↗